If the total defense of the armor after you have made it says 1000, then it'll be 1000. After you've made the runeword, any defense modifications on the armor itself (including the superior mod, and any defense values granted by the runeword) will already have taken into account for the armor. If you're enigma armor is indeed displaying 1000 defense, and you rolled a +760 defense from the enigma runeword, and the armor has 15% Enhanced Defense, then the armor's base defense was 209.

If you want to determine how much an enigma armor's defense will be, just remember that straight +defense is calculated after the % defense on the armor itself. So basically, it would be:

Base Armor Defense * Superior Defense + Straight Defense Bonus

So an enigma made in a 15% superior, 510 base defense archon plate would be (assuming you rolled +760 defense on the enigma runeword):